#!/bin/bash

# fst
vcftools --gzvcf 1.160500000-162500000.ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
--weir-fst-pop ../ref/1kgp_meta/EAS.txt \
--weir-fst-pop ../ref/1kgp_meta/YRI.txt \
--fst-window-size 20000 \
--out fcgr2b-it-EAS-YRI

# nucleotide diversity pi
vcftools --gzvcf 1.160500000-162500000.ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
--keep ../ref/1kgp_meta/EAS.txt \
--window-pi 20000 \
--out fcgr2b-it-EAS

# Tajima's D
vcftools --gzvcf 1.160500000-162500000.ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
--keep ../ref/1kgp_meta/EAS.txt \
--TajimaD 20000 \
--out fcgr2b-it-EAS
